dbSNP rs10426628: SULT2B1:c.423+1736A>G (chr19-48589173-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_177973.2(SULT2B1):c.423+1736A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 152,124 control chromosomes in the GnomAD database, including 47,121 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.77 ( 47121 hom., cov: 31)

Consequence

SULT2B1
NM_177973.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.26

Publications

15 publications found

Variant links:

Genes affected

SULT2B1 (HGNC:11459): (sulfotransferase family 2B member 1) Sulfotransferase enzymes catalyze the sulfate conjugation of many hormones, neurotransmitters, drugs, and xenobiotic compounds. These cytosolic enzymes are different in their tissue distributions and substrate specificities. The gene structure (number and length of exons) is similar among family members. This gene sulfates dehydroepiandrosterone but not 4-nitrophenol, a typical substrate for the phenol and estrogen sulfotransferase subfamilies. Two alternatively spliced variants that encode different isoforms have been described. [provided by RefSeq, Jul 2008]

SULT2B1 Gene-Disease associations (from GenCC):

ichthyosis, congenital, autosomal recessive 14
Inheritance: AR Classification: STRONG, LIMITED Submitted by: PanelApp Australia, Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
lamellar ichthyosis
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

SULT2B1 links:

ENSG00000287603 (HGNC:):

ENSG00000287603 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULT2B1	NM_177973.2 link	c.423+1736A>G		intron_variant	Intron 3 of 6	ENST00000201586.7	NP_814444.1	O00204-1
SULT2B1	NM_004605.2 link	c.378+1736A>G		intron_variant	Intron 2 of 5		NP_004596.2	O00204-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SULT2B1	ENST00000201586.7 link	c.423+1736A>G	intron_variant	Intron 3 of 6	1	NM_177973.2	ENSP00000201586.2	O00204-1
SULT2B1	ENST00000323090.4 link	c.378+1736A>G	intron_variant	Intron 2 of 5	1		ENSP00000312880.3	O00204-2
ENSG00000287603	ENST00000666424.1 link	n.493+7573T>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.774

AC:

117699

AN:

152006

Hom.:

47067

Cov.:

show subpopulations

Gnomad AFR

AF:

0.946

Gnomad AMI

AF:

0.686

Gnomad AMR

AF:

0.605

Gnomad ASJ

AF:

0.741

Gnomad EAS

AF:

0.481

Gnomad SAS

AF:

0.604

Gnomad FIN

AF:

0.614

Gnomad MID

AF:

0.759

Gnomad NFE

AF:

0.770

Gnomad OTH

AF:

0.779

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.774

AC:

117810

AN:

152124

Hom.:

47121

Cov.:

AF XY:

0.760

AC XY:

56560

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.946

AC:

39312

AN:

41544

American (AMR)

AF:

0.604

AC:

9230

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.741

AC:

2569

AN:

3468

East Asian (EAS)

AF:

0.480

AC:

2470

AN:

5148

South Asian (SAS)

AF:

0.606

AC:

2921

AN:

4824

European-Finnish (FIN)

AF:

0.614

AC:

6503

AN:

10584

Middle Eastern (MID)

AF:

0.765

AC:

225

AN:

294

European-Non Finnish (NFE)

AF:

0.770

AC:

52315

AN:

67962

Other (OTH)

AF:

0.777

AC:

1639

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1237

2474

3712

4949

6186

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

844

1688

2532

3376

4220

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.763

Hom.:

101539

Bravo

AF:

0.780

Asia WGS

AF:

0.591

AC:

2057

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

7.5

(source)

DANN

Benign

0.51

PhyloP100

-1.3

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over